NAOMInova

Overview

NAOMInova is a software tool enabling the geometrical and chemical analysis of atoms surrounding a user-defined structure of interest. Based on a user-selected set of protein structures, substructures can be searched and the distribution of partner points can be visualized. Two visualization options are available: the „set“ visualization, i.e. the partner points surrounding the substructure, and the „pocket“ visualization, i.e. the transformation of all partner points surrounding the substructure into a suitable active site of interest. Diverse geometric - distance, angles, resolution - and chemical - atom type, location, amino acid - properties can be selected for further analysis. Additionally, for each partner point the original complex is stored, which allows an easy evaluation whether this point is of interest for the user or not.

 

Download

NAOMInova is a part of the NAOMI ChemBio Suite. Our software is free for evaluation purposes and academic use.

Below, precompiled NAOMInova databases can be downloaded. The database containing PDBbind structures was used to analyze carbonyl interaction patterns (see reference 1). The second database contains 408 carbonic anhydrase structures. This database was used to analyze the interactions of carbonic anhydrase with its ligands and generate ideas to extend ligands. Please note that these databases are in a proprietary file format, they can only be used with the NAOMInova software.

- PDBbind version 2015, general set. Download here (~22 GB).

- Carbonic anhydrase, 408 structures. Download here (~75 MB).

People and References

[1] T. Inhester, et al. (2017). NAOMInova: Interactive Geometric Analysis of User-defined Substructures in Proteins. in preparation.

[2] E. Nittinger, et al. (2017). A Large-Scale Analysis of Hydrogen Bond Interaction Patterns in Protein-Ligand Interfaces. J. Med. Chem. Under revision